Chapter 9 Differential abundance analysis: functional
9.1 Wilcoxon
9.1.1 Community elements differences:
Elements high low Function
1 B0205 5.545938e-01 6.265510e-01 Amino acid biosynthesis_Threonine
2 B0208 6.271503e-01 7.060346e-01 Amino acid biosynthesis_Valine
3 B0210 6.016381e-01 6.799657e-01 Amino acid biosynthesis_Leucine
4 B0211 7.208532e-01 7.845367e-01 Amino acid biosynthesis_Lysine
5 B0212 5.374306e-01 6.135838e-01 Amino acid biosynthesis_Arginine
6 B0216 4.008679e-01 5.191861e-01 Amino acid biosynthesis_Tryptophan
7 B0217 3.860860e-01 4.488773e-01 Amino acid biosynthesis_Phenylalanine
8 B0218 3.110587e-01 3.672414e-01 Amino acid biosynthesis_Tyrosine
9 B0302 1.313611e-02 2.632273e-02 Amino acid derivative biosynthesis_Betaine
10 B0303 2.125935e-01 2.488038e-01 Amino acid derivative biosynthesis_Ectoine
11 B0309 7.951187e-02 9.738120e-02 Amino acid derivative biosynthesis_Putrescine
12 B0310 2.022088e-03 6.875040e-03 Amino acid derivative biosynthesis_Tryptamine
13 B0403 5.259044e-01 5.583029e-01 SCFA biosynthesis_Propionate
14 B0602 7.454626e-01 7.952110e-01 Organic anion biosynthesis_Fumarate
15 B0710 6.864721e-02 1.197774e-01 Vitamin biosynthesis_Phylloquinone (K1)
16 B0804 7.219838e-01 7.756036e-01 Aromatic compound biosynthesis_Dipicolinate
17 B0805 1.637677e-01 2.235599e-01 Aromatic compound biosynthesis_Indole-3-acetate
18 B0902 3.727339e-03 1.408047e-02 Metallophore biosynthesis_Aerobactin
19 B1012 3.984627e-02 2.523846e-02 Antibiotic biosynthesis_Fosfomycin
20 B1014 2.069216e-03 3.070448e-04 Antibiotic biosynthesis_Kanosamine
21 B1028 1.148606e-02 2.245694e-02 Antibiotic biosynthesis_Pyocyanin
22 B1029 4.284736e-04 1.457010e-06 Antibiotic biosynthesis_Pyrrolnitrin
23 D0104 1.242776e-01 1.799243e-01 Lipid degradation_Dicarboxylic acids
24 D0204 4.119183e-01 4.724725e-01 Polysaccharide degradation_Chitin
25 D0206 4.753334e-01 5.678805e-01 Polysaccharide degradation_Alpha galactan
26 D0211 8.531451e-02 1.122141e-01 Polysaccharide degradation_Alpha-mannan
27 D0213 2.955001e-01 3.571304e-01 Polysaccharide degradation_Mucin
28 D0301 1.478514e-02 3.667093e-02 Sugar degradation_Lactose
29 D0302 8.731257e-02 1.299471e-01 Sugar degradation_Sucrose
30 D0310 3.788951e-01 4.599128e-01 Sugar degradation_NeuAc
31 D0501 7.384596e-01 8.168574e-01 Amino acid degradation_Serine
32 D0502 2.960380e-01 3.904288e-01 Amino acid degradation_Threonine
33 D0508 3.114233e-02 7.625305e-02 Amino acid degradation_Lysine
34 D0603 6.322401e-03 1.820880e-02 Nitrogen compound degradation_Urate
35 D0604 5.681134e-01 6.013131e-01 Nitrogen compound degradation_GlcNAc
36 D0606 2.153605e-02 3.378014e-02 Nitrogen compound degradation_Allantoin
37 D0611 2.988320e-03 4.087332e-02 Nitrogen compound degradation_Phenylethylamine
38 D0701 9.514933e-03 1.967072e-02 Alcohol degradation_2,3-Butanediol
39 D0704 3.438279e-01 4.521028e-01 Alcohol degradation_Glycerol
40 D0709 1.302359e-05 6.776383e-04 Alcohol degradation_Polyvinyl alcohol
41 D0805 1.015905e-02 2.782693e-02 Xenobiotic degradation_Benzoate
42 D0807 3.385425e-02 6.491818e-02 Xenobiotic degradation_Catechol
43 D0815 3.794043e-06 2.070123e-04 Xenobiotic degradation_Phthalate
44 D0816 9.785049e-02 1.448659e-01 Xenobiotic degradation_Phenylacetate
45 D0903 3.822127e-02 1.095909e-01 Antibiotic degradation_Cephalosporin
46 D0906 1.585863e-06 2.020556e-04 Antibiotic degradation_Fosfomycin
47 D0910 4.777951e-01 5.764713e-01 Antibiotic degradation_Chloramphenicol
48 S0104 2.074062e-01 2.355010e-01 Cellular structure_Lipoteichoic acid
9.1.2 Community functions differences
Code_function high low Function
1 B02 0.52137130 0.5740600 Amino acid biosynthesis
2 B06 0.64729040 0.6917290 Organic anion biosynthesis
3 B08 0.41848200 0.4617373 Aromatic compound biosynthesis
4 D02 0.33806480 0.3876675 Polysaccharide degradation
5 D05 0.30239730 0.3394142 Amino acid degradation
6 D06 0.14482000 0.1610282 Nitrogen compound degradation
7 D08 0.01519399 0.0275254 Xenobiotic degradation
8 D09 0.18677310 0.2091800 Antibiotic degradation
9.2 ANCOM-BC2
9.2.2 Witho random effect
9.2.2.1 Element level
taxon lfc_environmentlow p_environmentlow Domain Function Element
1 B1014 -2.7787038 3.099009e-08 Biosynthesis Antibiotic biosynthesis_Kanosamine Kanosamine
2 B0805 0.2127575 2.004379e-02 Biosynthesis Aromatic compound biosynthesis_Indole-3-acetate Indole-3-acetate
3 D0104 0.2474646 1.314513e-02 Degradation Lipid degradation_Dicarboxylic acids Dicarboxylic acids
4 D0302 0.2863871 8.446544e-03 Degradation Sugar degradation_Sucrose Sucrose
5 B1028 0.4167257 1.612048e-02 Biosynthesis Antibiotic biosynthesis_Pyocyanin Pyocyanin
6 D0807 0.4763618 4.498157e-04 Degradation Xenobiotic degradation_Catechol Catechol
7 D0508 0.5163037 2.604708e-02 Degradation Amino acid degradation_Lysine Lysine
8 D0701 0.5375975 5.634684e-03 Degradation Alcohol degradation_2,3-Butanediol 2,3-Butanediol
9 B0302 0.5436327 1.828069e-02 Biosynthesis Amino acid derivative biosynthesis_Betaine Betaine
10 D0301 0.5948345 1.646718e-02 Degradation Sugar degradation_Lactose Lactose
11 B0902 0.6772208 3.927887e-02 Biosynthesis Metallophore biosynthesis_Aerobactin Aerobactin
12 D0805 0.6939341 6.786145e-03 Degradation Xenobiotic degradation_Benzoate Benzoate
13 D0517 0.6984238 1.645718e-02 Degradation Amino acid degradation_Ornithine Ornithine
14 D0903 0.7583944 4.002996e-03 Degradation Antibiotic degradation_Cephalosporin Cephalosporin
15 D0603 0.8707816 1.547040e-03 Degradation Nitrogen compound degradation_Urate Urate
16 B0310 1.4653554 3.161436e-04 Biosynthesis Amino acid derivative biosynthesis_Tryptamine Tryptamine
17 D0709 1.8839060 1.386329e-02 Degradation Alcohol degradation_Polyvinyl alcohol Polyvinyl alcohol
18 D0815 1.9151895 1.405453e-02 Degradation Xenobiotic degradation_Phthalate Phthalate
19 D0806 1.9633790 1.324239e-02 Degradation Xenobiotic degradation_Anthranilate Anthranilate